According to the apology, the magazine apologised for running the May 2009 special report, titled 'Tinjauan Al-Islam Dalam Gereja: Mencari Kesahihan Ramaja Melayu Murtad'.
Al-Islam said that the report had "unintentionally hurt the feelings of Christians especially Catholics".
The monthly magazine also explained that the report was to investigate allegations of apostasy and the actions of its journalists were never intended to deride the Christian faith, let alone desecrate their house of worship.
It stated that Al-Islam journalists who wrote the article also apologised for unintentionally hurting the feelings of Christians in the pursuit of their duty.
Malaysiakini was informed that Kuala Lumpur Catholic archbishop Murphy Pakiam has already been told about the apology. But attempts to contact Pakiam at his residence for comment has so far been unsuccessful.
Sources close to Utusan Karya, which is subsidiary of Umno-ownedUtusan Malaysia, said the apology was already in the works but it was delayed as they had to consult with lawyers about the legal ramifications.
This apology came following Thursday's press conference where Pakiam told reporters that the church would be satisfied if they received an apology from the magazine or its publishers over the matter.